Technical Abstract:
Recent advances in our understanding of silage microbiology are reviewed. The ability to extract microbial DNA from silages, amplify portions of DNA, and then separate those portions by the strains of microorganisms that have produced them has been at the core of the changes that have occurred recently in silage microbiology. These developments have allowed us to enumerate strains that do not grow on agar and reveal new species in silages. Most of these techniques use the polymerase chain reaction (PCR) to make many copies of a portion of the DNA in microorganisms. Both PCR and real-time PCR are being used to identify and quantify species involved in ensiling. In addition various PCR-based microbial community analysis techniques are being used: length heterogeneity PCR, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis and automated ribosomal intergenic spacer analysis. The new PCR-based techniques are uncovering some new species, both lactic acid bacteria as well as other bacteria and fungi. However, in most cases, traditional silage LAB species have been the dominant bacterial species present. Research is also giving us a clearer understanding of the microbial communities during the spoilage of silage. Yeast count has again been confirmed as the primary factor related to the initiation of heating and spoilage in most silages, and the yeast population is affected by both management issues (density and feed out rate) as well as silage fermentation products. Silage inoculants are widely available, and there is considerable research studying the effectiveness of various products. Of greater interest has been the research investigating why inoculants are so successful, both in the silo and in improving livestock performance (milk production, average daily gain, etc.). Many inoculant strains have been found to produce bacteriocins and other compounds that inhibit other bacteria and fungi. This may help explain why they can dominate silage fermentation even when substantially outnumbered at the beginning of fermentation. In vitro work is showing that the fermentation by rumen microorganisms of some inoculated silages is different than the fermentation of untreated silages. In some cases with inoculated silages, methane production is being reduced and in others rumen microbial biomass production is being increased. Both observations could explain improved milk production or gain on inoculated silage, but more research is needed to confirm and understand what is affecting the rumen microbial community. As we understand the microbiology in the silo, it will allow us to better manage as well as improve inoculants to enhance silage quality for our livestock.